Single-cell transcriptional atlas of the developing Drosophila visual system (V1.1)

An updated version of a single-cell transcriptional atlas of the developing Drosophila visual system (V1.1), originally published as GEO: GSE156455. Version V1.0 is available at: https://doi.org/10.5281/zenodo.8097374 

The manuscript describing the initial dataset (V1.0) is Kurmangaliyev et al., 2020: https://doi.org/10.1016/j.neuron.2020.10.006

The updates in V1.1 are described in Yoo et al., 2023: https://doi.org/10.1101/2023.04.03.534791

The updated Zenodo record provides a processed dataset at both the single-cell and cell-type/clusters levels (only the main dataset: 24-96hAPF).

Files included:

• data_V1.1a.rds: Seurat object (v3.1.2) with the processed and annotated dataset; stored as an R serialized file (RDS).
• expr_V1.1a.rds: Average gene expression per cell type/cluster and replicate in long-format (tidy) data frame; stored as an R serialized file (RDS).
• expr_V1.1a.tsv.gz: Average gene expression per cell type/cluster and replicate in long-format (tidy) data frame; provided as a TSV file.
• cell_types_V1.1a.tsv: Annotated clusters matched to cell-type labels in connectomic datasets, as in Nern et al., 2025 (https://doi.org/10.1038/s41586-025-08746-0). For Dm8, R1–6, and R7/8, one cluster corresponds to several connectomic cell types (separated by commas, e.g., "Dm8a,Dm8b").
• matrix_V1.1a.tar: Raw single-cell counts in 10X Genomics MTX format for the entire dataset (from data_V1.1a.rds); this directory also contains metadata.tsv.gz with single-cell-level metadata (from data_V1.1a.rds).

Metadata columns in average gene expression and single-cell metadata tables follow the original GSE156455 specification:

• set: dataset (W1118 or DGRP)
• rep: biological replicate
• time: developmental stage in hAPF (hours after puparium formation); 96h corresponds to freshly eclosed adult animals (0 days old)
• sample: combined sample identifier (set, rep, and time)
• class1: cell class (N, neurons; R, photoreceptors; G, glia; C, others)
• type2/subtype2: cell type or cluster identity for atlas V1.1. The type-subtype hierarchy is defined only for T4/T5 and Dm3 subtypes; for all other clusters, type and subtype are the same. We recommend using subtype2 as the default cluster identity.
• n: number of cells for a given cell type/cluster and replicate (average expression tables only)
• gene: gene symbol based on FlyBase release 6.29 (average expression tables only)
• expr: average normalized gene expression value in TP10K (transcripts per 10,000 UMIs; average expression tables only)

Additional metadata columns for single-cell tables only:

• trep: technical replicate (single 10X library)
• genotype: DGRP strain or W1118
• cluster0: original cluster identities (before cell-type annotation)
• type1/subtype1: cell type or cluster identity for atlas V1.0